[CP2K-user] [CP2K:16862] CP2K to study ORR mechanism for MOFs
DMITRII Drugov
dresearcher1991 at gmail.com
Sat Apr 16 02:13:06 UTC 2022
Dear Anton,
Thank you for your reply and valuable prospective on electronic state of
Co-doped ZIF-8 system.
I had to optimised Zn:Co ration to 9:1, so for that cell I used only 1 Co
atom.
But I have to redo everything from the begging to build correct slabs.
Do you think DOS profile will be the same for 011 and 001 terminated cell
built from the same cif file?
Best,
Dmitrii
On Friday, April 8, 2022 at 7:00:14 PM UTC+10 anton.s.l... at gmail.com wrote:
> Dear Dmitrii,
>
> чт, 7 квіт. 2022 р. о 16:22 DMITRII Drugov <dresear... at gmail.com> пише:
>
>> Therefore, I thought about which active site of the terminated surface I
>> need to consider for adsorption of intermediates, metals or its ligands?
>>
> I don't know which list of intermediates you are about to consider. I
> think you should write the list according to the literature and the
> chemical intuition, then think about which kinds of ZIF atoms and/or ions
> could exhibit specific interactions with these species. It is possible that
> separate preliminary calculations are necessary, I am not so familiar with
> the field.
>
> Do you think to estimate the right multiplicity I need to consider the
>> correct number of unpaired electrons for the whole Co-doped ZIF-8 unit cell?
>>
> How many Co ions per unit cell do you model? I've seen 1 in the file, is
> it true?
>
> Each of them can have either 3 or 1 unpaired electron, depending on the
> ligand field strength (as I've told, you have to consult the literature to
> figure out if Co(II) is low-spin or high-spin in this coordination
> environment). If they are not involved in the strong antiferromagnetic
> interaction [10.1098/rspa.1952.0181] (as you "dilute" your Co ions with
> diamagnetic Zn2+, they are definitely are not), the final number of the
> unpaired electrons is just a sum of their numbers at each Co2+ ion in the
> cell.
>
> Relax multiplicity can give me a rough idea for this number?
>>
> Yes.
>
> Anton
>
> On Thu, Apr 7, 2022 at 7:32 PM Anton Lytvynenko <anton.s.l... at gmail.com>
> wrote:
>
>> Dear Dmitrii,
>>
>> пт, 1 квіт. 2022 р. о 16:09 DMITRII Drugov <dresear... at gmail.com> пише:
>>
>>> I set up LSD and multiplicity 2 only because I directly create a slab
>>> 011 from cif of zif-8 by Avogadro software.
>>
>> It is not the correct way. Indeed, you need an odd number of electrons,
>> but it does not mean that you may put any even multiplicity here. Co2+ in
>> this coordination environment has an exact preferred multiplicity, you can
>> deduce it from the literature -- just search for complexes of Co(II) with
>> the same environment in literature or refer to the "Comprehensive
>> Coordination Chemistry" book. I am out of the topic for some time, but I
>> guess the multiplicity will be 4 (you should check it by yourself anyway).
>> As you have only one Co ion per a pretty large cell, this should be enough
>> (a few close paramagnetic ions would complicate the task sending you
>> directly into the realm of magnetochemistry). Anyway, if in doubt or there
>> is no data, please employ the relax_multiplicity feature of CP2k -- at
>> least for a preliminary run to deduce the correct multiplicity.
>>
>> Regarding the slabs, unfortunately I can't help here at the moment. To
>> get CP2k working correctly, you definitely need to generate all atoms
>> needed to form the slab (without gaps), all of them must be unique with
>> respect to translations of the slab supercell and all bonds must be
>> correctly terminated (either with explicitly declared atom or with a
>> replica obtained by the translations). Maybe there is a program that does
>> it correctly, but I am afraid some homebrew code will be needed, and I am
>> unable to produce it immediately (despite I also need it for some other
>> tasks).
>>
>>
>>> Do you think when I do reaction coordinate studies according to CHE
>>> method, should I consider only metal as an absorption site or nitrogen atom
>>> of imidazolium ligand as well? Ideally I would chose only one adsorption
>>> center.
>>>
>> What do you mean under CHE method?
>>
>> Adsorption of what?
>>
>> Yours,
>> Anton
>>
>>
>>> On Friday, April 1, 2022 at 10:46:11 PM UTC+10 anton.s.l... at gmail.com
>>> wrote:
>>>
>>>> Dear Dmitrii,
>>>>
>>>> how did you obtain the xyz? Did you just export it from CIF? It looks
>>>> like it is full of disordered hydrogen atoms.
>>>>
>>>> MULTIPLICITY 2
>>>>>
>>>> Are you sure?
>>>>
>>>> What do you think I need to change for energy calculations, expect of
>>>>> deeper EPS_SCF from 1.0E-6 to 1.0E-7 or -8?
>>>>>
>>>> I don't know. AFAIR, the default is 1e-5, I used to lower it to 1e-6,
>>>> while 1.0e-7 resulted in very slow convergence (I mean that the calculation
>>>> reached the residues of ca 1e-6 and then started to turning around it,
>>>> until "accidentally" reached 1e-7 -- I guess that some other parameters are
>>>> to be tuned to avoid numeric noise). Anyway, you always could check the
>>>> consistency w.r.t. to the considered parameter by yourself. The key point
>>>> in your case is to get rid of numeric noise in gradients -- you can assess
>>>> it via observing the course of your geometry optimization (if you see some
>>>> random moves around the equilibrium rather than smooth convergence to it,
>>>> this might be the case).
>>>>
>>>> Do I need to use spin polarisation for Co and Zn atoms when I calculate
>>>>> adsorption energy for ORR reaction coordinate, or I can reach desirably
>>>>> accuracy without it? My job is to compare different facets reactivity for
>>>>> ORR.
>>>>>
>>>> I probably don't understand your question. If your system is
>>>> paramagnetic, you have to use the spin-unrestricted formalism (LSD aka UKS)
>>>> anyway.
>>>>
>>>> I don't think the idea of crystallographic facets makes real sense in
>>>> the case of MOFs. The active centers in the case of MOFs are either the
>>>> metal ions with the coordinated atoms, or the fragments of ligands, these
>>>> centers are unlikely to be affected if you change the facet.
>>>>
>>>> Yours,
>>>> Anton
>>>>
>>>> нд, 27 бер. 2022 р. о 08:47 DMITRII Drugov <dresear... at gmail.com> пише:
>>>>
>>>>> Dear Anton,
>>>>>
>>>>> Thank you for your reply.
>>>>> I even did not think about low symmetry of MOFs. Thank you for this
>>>>> point.
>>>>> I attach my input file below for cell_opt first, then I will do energy
>>>>> calculation.
>>>>> Could you please have a look at my settings and express your opinion
>>>>> on its accuracy?
>>>>> What do you think I need to change for energy calculations, expect of
>>>>> deeper EPS_SCF from 1.0E-6 to 1.0E-7 or -8?
>>>>> Do I need to use spin polarisation for Co and Zn atoms when I
>>>>> calculate adsorption energy for ORR reaction coordinate, or I can reach
>>>>> desirably accuracy without it? My job is to compare different facets
>>>>> reactivity for ORR.
>>>>>
>>>>> Best,
>>>>> Dmitrii
>>>>>
>>>>> &GLOBAL
>>>>> PROJECT MOF_011_optimisation_larger_cell
>>>>> RUN_TYPE CELL_OPT
>>>>> PRINT_LEVEL MEDIUM
>>>>> !EXTENDED_FFT_LENGTHS
>>>>> &END GLOBAL
>>>>> &FORCE_EVAL
>>>>> STRESS_TENSOR ANALYTICAL
>>>>> METHOD QS
>>>>> &DFT
>>>>> BASIS_SET_FILE_NAME BASIS_MOLOPT
>>>>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>>>>> LSD
>>>>> CHARGE 0
>>>>> MULTIPLICITY 2
>>>>> &MGRID
>>>>> CUTOFF 800
>>>>> NGRIDS 5
>>>>> REL_CUTOFF 70
>>>>> &END MGRID
>>>>> &QS
>>>>> EPS_DEFAULT 1.0E-14
>>>>> !WF_INTERPOLATION ASPC
>>>>> &END QS
>>>>> &SCF
>>>>> SCF_GUESS ATOMIC
>>>>> EPS_SCF 1.0E-6
>>>>> MAX_SCF 300
>>>>> &OT
>>>>> MINIMIZER CG
>>>>> PRECONDITIONER FULL_KINETIC
>>>>> # ENERGY_GAP 0.01
>>>>> &END OT
>>>>> &OUTER_SCF
>>>>> EPS_SCF 1E-6
>>>>> MAX_SCF 300
>>>>> &END
>>>>> !CHOLESKY INVERSE
>>>>> !ADDED_MOS 100
>>>>> !&SMEAR ON
>>>>> ! METHOD FERMI_DIRAC
>>>>> ! ELECTRONIC_TEMPERATURE [K] 1000
>>>>> ! &END SMEAR
>>>>> !&DIAGONALIZATION
>>>>> ! ALGORITHM STANDARD
>>>>> !&END DIAGONALIZATION
>>>>> !&MIXING
>>>>> ! METHOD BROYDEN_MIXING
>>>>> !ALPHA 0.4
>>>>> !NBROYDEN 8
>>>>> !&END MIXING
>>>>> &END SCF
>>>>> &XC
>>>>> &XC_FUNCTIONAL
>>>>> &PBE
>>>>> &END PBE
>>>>> &END XC_FUNCTIONAL
>>>>> &vdW_POTENTIAL
>>>>> DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>>>>> &PAIR_POTENTIAL
>>>>> PARAMETER_FILE_NAME dftd3.dat
>>>>> TYPE DFTD3
>>>>> REFERENCE_FUNCTIONAL PBE
>>>>> R_CUTOFF 8.0
>>>>> &END PAIR_POTENTIAL
>>>>> &END vdW_POTENTIAL
>>>>> &END XC
>>>>> SURFACE_DIPOLE_CORRECTION T
>>>>> SURF_DIP_DIR Z
>>>>> &POISSON
>>>>> PERIODIC xy
>>>>> POISSON_SOLVER ANALYTIC
>>>>> &END POISSON
>>>>> &END DFT
>>>>> &SUBSYS
>>>>> &CELL
>>>>> ABC 18.55406 16.35222 50
>>>>> ALPHA_BETA_GAMMA 90.0 90.0 90.0
>>>>> PERIODIC xy
>>>>> SYMMETRY ORTHORHOMBIC
>>>>> &END CELL
>>>>> &COORD
>>>>> C 2.69109 3.50908 2.31039
>>>>> C 2.69109 12.34314 2.31039
>>>>> C 0.51227 7.92611 3.89871
>>>>> N 5.94837 3.44592 0.26929
>>>>> N 1.20316 9.05092 3.62466
>>>>> N 1.20316 6.8013 3.62466
>>>>> N 5.94837 12.4063 0.26929
>>>>> C 6.87686 10.39498 0
>>>>> C 5.92646 4.78521 0.67203
>>>>> C 2.43496 8.59814 3.1409
>>>>> C 2.43496 7.25408 3.1409
>>>>> C 6.87686 5.45724 0
>>>>> C 5.92646 11.06701 0.67203
>>>>> H 7.0639 9.48822 0.08937
>>>>> H 5.34848 5.15102 1.30235
>>>>> H 3.13933 9.1391 2.86446
>>>>> H 3.13933 6.71312 2.86446
>>>>> H 7.0639 6.364 0.08937
>>>>> H 5.34848 10.7012 1.30235
>>>>> C 2.26139 4.168 1.04379
>>>>> C 2.26139 11.68422 1.04379
>>>>> H 1.56208 4.79832 1.23086
>>>>> H 2.83938 11.95708 0.32767
>>>>> H 1.56208 11.0539 1.23086
>>>>> H 2.83938 3.89514 0.32767
>>>>> H 3.00789 4.62555 0.65058
>>>>> H 2.30689 10.73099 1.14626
>>>>> H 3.00789 11.22667 0.65058
>>>>> H 2.30689 5.12123 1.14626
>>>>> H 1.93449 3.50312 0.43134
>>>>> H 1.35819 11.94159 0.83884
>>>>> H 1.93449 12.3491 0.43134
>>>>> H 1.35819 3.91063 0.83884
>>>>> O 5.79166 7.92611 2.27822
>>>>> Zn 4.81431 13.8838 0.89604
>>>>> Zn 0.60158 10.90496 3.87488
>>>>> C 6.93752 15.29816 2.4367
>>>>> C 0.69089 10.88113 6.85373
>>>>> N 3.68024 13.25705 2.37354
>>>>> N 2.08951 12.13224 3.49836
>>>>> N 0 11.15518 5.72892
>>>>> N 5.94837 15.36131 1.52279
>>>>> C 3.70215 13.65979 3.71283
>>>>> C 2.75175 12.98777 4.38486
>>>>> H 4.28013 14.29012 4.07864
>>>>> H 6.48928 15.85222 5.64074
>>>>> H 2.56471 13.07713 5.29162
>>>>> C 7.36722 14.03155 3.09562
>>>>> C 2.05244 10.27344 6.85373
>>>>> H 2.83938 15.81052 1.4644
>>>>> H 8.06653 14.21863 3.72594
>>>>> H 2.36587 10.18765 5.95054
>>>>> H 6.78923 13.31544 2.82276
>>>>> H 6.62072 13.63835 3.55317
>>>>> H 2.65402 10.83346 6.35805
>>>>> H 7.32172 14.13403 4.04885
>>>>> H 1.35819 15.82601 0.95323
>>>>> H 1.93449 15.4185 1.36074
>>>>> H 7.69412 13.4191 2.43074
>>>>> H 2.01537 9.40362 6.44622
>>>>> H 8.27042 13.82661 2.83825
>>>>> O 3.83695 15.26599 6.85373
>>>>> O 5.92646 12.31097 6.85373
>>>>> Co 0.60158 4.94726 3.87488
>>>>> Zn 4.81431 1.96842 0.89604
>>>>> C 6.93752 0.55406 2.4367
>>>>> C 0.69089 4.97109 6.85373
>>>>> N 2.08951 3.71998 3.49836
>>>>> N 3.68024 2.59517 2.37354
>>>>> N 5.94837 0.49091 1.52279
>>>>> N 0 4.69704 5.72892
>>>>> C 2.75175 2.86445 4.38486
>>>>> C 3.70215 2.19243 3.71283
>>>>> H 2.56471 2.77509 5.29162
>>>>> H 6.48928 0 5.64074
>>>>> H 4.28013 1.5621 4.07864
>>>>> C 7.36722 1.82067 3.09562
>>>>> C 2.05244 5.57878 6.85373
>>>>> H 2.83938 0.0417 1.4644
>>>>> H 6.78923 2.53678 2.82276
>>>>> H 2.36587 5.66457 5.95054
>>>>> H 8.06653 1.63359 3.72594
>>>>> H 7.32172 1.71819 4.04885
>>>>> H 2.65402 5.01876 6.35805
>>>>> H 6.62072 2.21387 3.55317
>>>>> H 1.93449 0.43372 1.36074
>>>>> H 1.35819 0.02621 0.95323
>>>>> H 8.27042 2.02561 2.83825
>>>>> H 2.01537 6.4486 6.44622
>>>>> H 7.69412 2.43312 2.43074
>>>>> O 3.83695 0.58623 6.85373
>>>>> O 5.92646 3.54125 6.85373
>>>>> C 17.36317 7.92611 3.89871
>>>>> N 15.96455 4.57074 2.6476
>>>>> N 14.37382 12.4063 1.52279
>>>>> N 15.96455 11.28148 2.6476
>>>>> N 14.37382 3.44592 1.52279
>>>>> N 18.05406 9.05092 3.62466
>>>>> N 18.05406 6.8013 3.62466
>>>>> C 15.30231 5.45724 1.79207
>>>>> C 14.35191 11.06701 1.12005
>>>>> C 15.30231 10.39498 1.79207
>>>>> C 14.35191 4.78521 1.12005
>>>>> H 15.48935 6.364 1.70271
>>>>> H 13.77393 10.7012 0.48972
>>>>> H 15.48935 9.48822 1.70271
>>>>> H 13.77393 5.15102 0.48972
>>>>> C 10.68684 11.68422 0.74829
>>>>> C 10.68684 4.168 0.74829
>>>>> C 16.00162 7.92611 4.5064
>>>>> H 9.98753 11.0539 0.56121
>>>>> H 11.26483 3.89514 1.4644
>>>>> H 15.68819 8.8293 4.59219
>>>>> H 15.68819 7.02292 4.59219
>>>>> H 9.98753 4.79832 0.56121
>>>>> H 11.26483 11.95708 1.4644
>>>>> H 11.43334 11.22667 1.14149
>>>>> H 10.73234 5.12123 0.64581
>>>>> H 15.40004 7.43043 3.94638
>>>>> H 15.40004 8.42179 3.94638
>>>>> H 11.43334 4.62555 1.14149
>>>>> H 10.73234 10.73099 0.64581
>>>>> H 10.35994 12.3491 1.36074
>>>>> H 9.78364 3.91063 0.95323
>>>>> H 16.03869 7.5186 5.37622
>>>>> H 16.03869 8.33362 5.37622
>>>>> H 10.35994 3.50312 1.36074
>>>>> H 9.78364 11.94159 0.95323
>>>>> O 12.1276 7.92611 2.46887
>>>>> Zn 13.23976 13.8838 0.89604
>>>>> Zn 17.45248 10.90496 3.87488
>>>>> C 15.36297 12.46945 2.4367
>>>>> C 11.11654 15.42446 2.31039
>>>>> C 17.54179 10.88113 6.85373
>>>>> N 14.37382 15.36131 0.26929
>>>>> N 10.51496 15.63536 3.49836
>>>>> N 16.8509 11.15518 5.72892
>>>>> N 12.10569 14.51055 2.37354
>>>>> C 11.1772 14.77984 4.38486
>>>>> C 15.6191 11.63894 6.1817
>>>>> C 12.1276 14.10781 3.71283
>>>>> H 10.99016 14.69047 5.29162
>>>>> H 14.91473 11.91538 5.64074
>>>>> H 12.70558 13.47749 4.07864
>>>>> C 15.79267 13.73605 3.09562
>>>>> H 15.21468 14.45217 2.82276
>>>>> H 16.49198 13.54898 3.72594
>>>>> H 11.26483 15.81052 0.32767
>>>>> H 15.74717 13.63358 4.04885
>>>>> H 15.04617 14.12926 3.55317
>>>>> H 16.69587 13.941 2.83825
>>>>> H 16.11957 14.3485 2.43074
>>>>> H 10.35994 15.4185 0.43134
>>>>> H 9.78364 15.82601 0.83884
>>>>> O 12.2624 12.50162 6.85373
>>>>> O 14.35191 15.45663 6.85373
>>>>> Zn 17.45248 4.94726 3.87488
>>>>> Zn 13.23976 1.96842 0.89604
>>>>> C 15.36297 3.38277 2.4367
>>>>> C 11.11654 0.42776 2.31039
>>>>> C 17.54179 4.97109 6.85373
>>>>> N 14.37382 0.49091 0.26929
>>>>> N 12.10569 1.34167 2.37354
>>>>> N 16.8509 4.69704 5.72892
>>>>> N 10.51496 0.21686 3.49836
>>>>> C 12.1276 1.74441 3.71283
>>>>> C 15.6191 4.21328 6.1817
>>>>> C 11.1772 1.07238 4.38486
>>>>> H 12.70558 2.37473 4.07864
>>>>> H 14.91473 3.93684 5.64074
>>>>> H 10.99016 1.16175 5.29162
>>>>> C 15.79267 2.11617 3.09562
>>>>> H 16.49198 2.30324 3.72594
>>>>> H 15.21468 1.40005 2.82276
>>>>> H 11.26483 0.0417 0.32767
>>>>> H 15.04617 1.72296 3.55317
>>>>> H 15.74717 2.21864 4.04885
>>>>> H 16.11957 1.50372 2.43074
>>>>> H 16.69587 1.91122 2.83825
>>>>> H 9.78364 0.02621 0.83884
>>>>> H 10.35994 0.43372 0.43134
>>>>> O 12.2624 3.3506 6.85373
>>>>> O 14.35191 0.39559 6.85373
>>>>> &END COORD
>>>>> &KIND Co
>>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>>> POTENTIAL GTH-PBE-q17
>>>>> &END KIND
>>>>> &KIND Zn
>>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>>> POTENTIAL GTH-PBE-q12
>>>>> &END KIND
>>>>> &KIND O
>>>>> BASIS_SET TZVP-MOLOPT-GTH
>>>>> POTENTIAL GTH-PBE-q6
>>>>> &END KIND
>>>>> &KIND C
>>>>> BASIS_SET TZVP-MOLOPT-GTH
>>>>> POTENTIAL GTH-PBE-q4
>>>>> &END KIND
>>>>> &KIND H
>>>>> BASIS_SET TZVP-MOLOPT-GTH
>>>>> POTENTIAL GTH-PBE-q1
>>>>> &END KIND
>>>>> &KIND N
>>>>> BASIS_SET TZVP-MOLOPT-GTH
>>>>> POTENTIAL GTH-PBE-q5
>>>>> &END KIND
>>>>> &END SUBSYS
>>>>> &END FORCE_EVAL
>>>>> &MOTION
>>>>> &GEO_OPT
>>>>> OPTIMIZER LBFGS
>>>>> MAX_ITER 300
>>>>> &END GEO_OPT
>>>>> &CELL_OPT
>>>>> EXTERNAL_PRESSURE [bar] 0.0
>>>>> KEEP_ANGLES TRUE
>>>>> KEEP_SYMMETRY TRUE
>>>>> OPTIMIZER LBFGS
>>>>> &END
>>>>> &END MOTION
>>>>> &END
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Friday, March 25, 2022 at 8:32:42 PM UTC+10 anton.s.l... at gmail.com
>>>>> wrote:
>>>>>
>>>>>> Dear Dmitrii,
>>>>>>
>>>>>> CP2k has implementation of k-points, but it could be incompatible
>>>>>> with some methods and features.
>>>>>>
>>>>>> But why do you need it? MOFs cells are typically large and have low
>>>>>> symmetry.
>>>>>>
>>>>>> Yours,
>>>>>> Anton
>>>>>>
>>>>>> пт, 25 бер. 2022 р. о 10:38 DMITRII Drugov <dresear... at gmail.com>
>>>>>> пише:
>>>>>>
>>>>>>> Dear CP2K users,
>>>>>>>
>>>>>>> Could you please share your thoughts on correct CP2K settings to
>>>>>>> study oxygen reaction reaction on MOFs surface (186 atoms, C, H, O, N, Zn)?
>>>>>>> I used to conduct similar job on Quantum Espresso for to study HER on
>>>>>>> graphite slab (86 atoms) and it took ages to finish single energy
>>>>>>> calculation with soft potentials (ecutrho = 0.4000000000d+03
>>>>>>> ecutwfc = 0.5000000000d+02). According to my experience at gamma
>>>>>>> point CP2K is much faster but I never added k-point mesh to CP2K.
>>>>>>> Could you please let me know what my CP2K should be? Does CP2K allow
>>>>>>> to set up k-points for energy calculation? My system is a slab with vacuum
>>>>>>> of 2*x or y in z dimension.
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Dmitrii
>>>>>>>
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